Group method

conformance/tests/ot_group.py

@@ -0,0 +1,32 @@
+from __future__ import absolute_import
+
+import gripql
+
+def test_childGroups(man):
+    errors = []
+    G = man.setGraph("swapi")
+
+    mapping = {
+        'Planet:1' : ['Luke Skywalker', 'C-3PO', 'Darth Vader', 'Owen Lars', 'Beru Whitesun lars', 'R5-D4', 'Biggs Darklighter'],
+        'Planet:2' :  ['Leia Organa', 'Raymus Antilles']
+    }
+    mapping_hair = {
+        'Planet:1' : ["blond", None, "none", "brown, grey", "brown", None, "black"],
+        'Planet:2' : ["brown", "brown"]
+    }
+
+    for i in G.query().V().hasLabel("Planet").as_("planet").out("residents").as_("character").select("planet").group( {"people" : "$character.name"}  ):
+        #print(i)
+        if sorted(i["data"]["people"]) != sorted(mapping[i["gid"]]):
+            errors.append("grouped output not equal: %s != %s" % (sorted(i["data"]["people"]) , sorted(mapping[i["gid"]])))
+
+    for i in G.query().V().hasLabel("Planet").as_("planet").out("residents").as_("character").select("planet").group( 
+        {"people" : "$character.name", "hair":"$character.hair_color"}  ):
+        #print(i)
+        print(i["data"])
+        if sorted(i["data"]["people"]) != sorted(mapping[i["gid"]]):
+            errors.append("grouped output not equal: %s != %s" % (sorted(i["data"]["people"]) , sorted(mapping[i["gid"]])))
+
+        if sorted(i["data"]["hair"], key=lambda x: (x is None, x)) != sorted(mapping_hair[i["gid"]], key=lambda x: (x is None, x)):
+            errors.append("grouped output not equal: %s != %s" % (sorted(i["data"]["hair"], key=lambda x: (x is None, x)) , sorted(mapping_hair[i["gid"]], key=lambda x: (x is None, x))))  
+    return errors

conformance/tests/ot_totype.py

@@ -0,0 +1,62 @@
+import gripql
+
+def test_totype(man):
+    errors = []
+
+    G = man.setGraph("swapi")
+
+    q = G.query().V().hasLabel("Character").totype("birth_year", "string").totype("eye_color", "float").totype("hair_color", "int").totype("skin_color", "list").totype("mass", "string").execute()
+    if len(q) == 0:
+        errors.append("ERROR, q returns no items")
+    for row in q:
+        data = row["data"]
+        # transforms that should work
+        if not isinstance(data["birth_year"], str):
+            errors.append("string field %s should be string" % (data["birth_year"]))
+        if not isinstance(data["skin_color"], list):
+            errors.append("string field %s should be list" % (data["skin_color"]))
+        # some masses are none by default
+        if data["mass"] is not None and not isinstance(data["mass"], str):
+            errors.append("int field %d should be string" % (data["mass"]))
+
+        # transforms that shouldn't work'
+        if data["eye_color"] != 0.0:
+            errors.append("string value %s should be 0.0" % (data["eye_color"]))
+        if data["hair_color"] != 0:
+            errors.append("%s should be 0" % (data["hair_color"]))
+
+    r = G.query().V().hasLabel("Starship").totype("hyperdrive_rating", "string").totype("length", "int").totype("length", "float").totype("system", "list").execute()
+    if len(r) == 0:
+        errors.append("ERROR, r returns no items")
+    for row in r:
+        data = row["data"]
+        if  isinstance(data["hyperdrive_rating"], int) or isinstance(data["hyperdrive_rating"], float):
+            errors.append("float field %s should be int or float" %(data["hyperdrive_rating"]))
+        if not isinstance(data["length"], int):
+            errors.append("float field %s should be int" %(data["length"]))
+        if not isinstance(data["system"], list):
+            errors.append("dict object with key 'system' %s should be list" %(data["system"]))
+
+    s = G.query().V().hasLabel("Species").totype("system.created", "bool").execute()
+    if len(s) == 0:
+        errors.append("ERROR, s returns no items")
+    for row in s:
+        data = row["data"]
+        if data["system"]["created"] != True:
+            errors.append("string %s to bool should be False" %(data["system"]["created"]))
+
+
+    t = G.query().V().hasLabel("Starship").totype("MGLT", "bool").totype("eye_colors", "int").totype("classification", "int").execute()
+    if len(t) == 0:
+        errors.append("ERROR, t returns no items")
+
+    for row in t:
+        data = row["data"]
+        if data["length"] is False:
+            errors.append("int %s to bool should be True" %(data["MGLT"]))
+        if data["eye_colors"] != 0:
+            errors.append("list %s to bool should be False" %(data["eye_colors"]))
+        if data["classification"] !=  0:
+            errors.append("string %s to bool should be False" %(data["classification"]))
+
+    return errors

conformance/tests/ot_transform.py

@@ -46,3 +46,24 @@ def test_unwind(man):
         errors.append("There should be 2 vertices after unwind process and filter")
 
     return errors
+
+
+def test_unwind_group_totype(man):
+    errors = []
+    G = man.writeTest()
+    bulk = G.bulkAdd()
+    bulk.addVertex("1", "Observation", {"resourceType": "Observation", "id": "e87cecef-c91d-3861-a35e-6eaed41580c8", "status": "final", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory", "display": "laboratory"}]}], "code": {"coding": [{"system": "http://loinc.org", "code": "81247-9", "display": "Master HL7 genetic variant reporting panel"}]}, "subject": {"reference": "Patient/ac0d7a82-82cb-4aec-b859-e37375f3de8b"}, "specimen": {"reference": "Specimen/dc48f578-193c-4740-93f3-61a78e3c6ba0"}, "focus": [{"reference": "Specimen/dc48f578-193c-4740-93f3-61a78e3c6ba0"}], "effectiveDateTime": "2024-06-03T08:00:00+00:00", "valueString": "Sequencing parameters", "component": [{"code": {"coding": [{"system": "https://cadsr.cancer.gov/sample_laboratory_observation", "code": "concentration", "display": "concentration"}], "text": "concentration"}, "valueQuantity": {"value": 0.16}}, {"code": {"coding": [{"system": "https://cadsr.cancer.gov/sample_laboratory_observation", "code": "aliquot_quantity", "display": "aliquot_quantity"}], "text": "aliquot_quantity"}, "valueQuantity": {"value": 2.13}}, {"code": {"coding": [{"system": "https://cadsr.cancer.gov/sample_laboratory_observation", "code": "aliquot_volume", "display": "aliquot_volume"}], "text": "aliquot_volume"}, "valueQuantity": {"value": 13.3}}]})
+
+    bulk.addVertex("2", "Specimen", {"resourceType": "Specimen", "id": "dc48f578-193c-4740-93f3-61a78e3c6ba0", "status": "final", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory", "display": "laboratory"}]}], "code": {"coding": [{"system": "http://loinc.org", "code": "81247-9", "display": "Master HL7 genetic variant reporting panel"}]}, "subject": {"reference": "Patient/ac0d7a82-82cb-4aec-b859-e37375f3de8b"}, "specimen": {"reference": "Specimen/dc48f578-193c-4740-93f3-61a78e3c6ba0"}, "focus": [{"reference": "Specimen/dc48f578-193c-4740-93f3-61a78e3c6ba0"}], "effectiveDateTime": "2024-06-03T08:00:00+00:00", "valueString": "Sequencing parameters", "component": [{"code": {"coding": [{"system": "https://cadsr.cancer.gov/sample_laboratory_observation1", "code": "concentration", "display": "concentration"}], "text": "concentration"}, "valueQuantity": {"value": 0.16}}, {"code": {"coding": [{"system": "https://cadsr.cancer.gov/sample_laboratory_observation2", "code": "aliquot_quantity", "display": "aliquot_quantity"}], "text": "aliquot_quantity"}, "valueQuantity": {"value": 2.13}}, {"code": {"coding": [{"system": "https://cadsr.cancer.gov/sample_laboratory_observation3", "code": "aliquot_volume", "display": "aliquot_volume"}], "text": "aliquot_volume"}, "valueQuantity": {"value": 13.3}}]})
+    bulk.addEdge("1", "2", "focus_Specimen")
+    err = bulk.execute()
+
+    orig_row = {}
+    for i in G.query().V().hasLabel("Observation").as_("f0").out("focus_Specimen"):
+        orig_row = i
+
+    for i in G.query().V().hasLabel("Observation").as_("f0").out("focus_Specimen").unwind("component").unwind("component.code.coding").as_("f1").totype("$f1.component.code.coding","list").group({"component":"$f1.component"}):
+        if not isinstance(i["data"]["component"][0]["code"]["coding"], list) and  isinstance(orig_row["data"]["component"][0]["code"]["coding"], list):
+            errors.append("Original row list format not preserved: %s !=\n\n %s" % (orig_row, i))
+
+    return errors

docs/categories/index.xml

@@ -4,7 +4,7 @@
     <title>Categories on GRIP</title>
     <link>https://bmeg.github.io/grip/categories/</link>
     <description>Recent content in Categories on GRIP</description>
-    <generator>Hugo</generator>
+    <generator>Hugo -- gohugo.io</generator>
     <language>en-us</language>
     <atom:link href="https://bmeg.github.io/grip/categories/index.xml" rel="self" type="application/rss+xml" />
   </channel>

docs/docs/queries/jsonpath/index.html

@@ -394,50 +394,50 @@ <h1 id="referencing-vertexedge-properties">Referencing Vertex/Edge Properties</h
 }
 </code></pre><p>Below is a table of field and the values they would reference in subsequent traversal operations.</p>
 <table>
-  <thead>
-      <tr>
-          <th style="text-align: left">jsonpath</th>
-          <th style="text-align: left">result</th>
-      </tr>
-  </thead>
-  <tbody>
-      <tr>
-          <td style="text-align: left">_gid</td>
-          <td style="text-align: left">&ldquo;NM_007294.3:c.4963_4981delTGGCCTGACCCCAGAAG&rdquo;</td>
-      </tr>
-      <tr>
-          <td style="text-align: left">_label</td>
-          <td style="text-align: left">&ldquo;variant&rdquo;</td>
-      </tr>
-      <tr>
-          <td style="text-align: left">_data.type</td>
-          <td style="text-align: left">&ldquo;deletion&rdquo;</td>
-      </tr>
-      <tr>
-          <td style="text-align: left">type</td>
-          <td style="text-align: left">&ldquo;deletion&rdquo;</td>
-      </tr>
-      <tr>
-          <td style="text-align: left">publications[0].pmid</td>
-          <td style="text-align: left">29480828</td>
-      </tr>
-      <tr>
-          <td style="text-align: left">publications[:].pmid</td>
-          <td style="text-align: left">[29480828, 23666017]</td>
-      </tr>
-      <tr>
-          <td style="text-align: left">publications.pmid</td>
-          <td style="text-align: left">[29480828, 23666017]</td>
-      </tr>
-      <tr>
-          <td style="text-align: left">$gene.symbol.hugo</td>
-          <td style="text-align: left">&ldquo;BRCA1&rdquo;</td>
-      </tr>
-      <tr>
-          <td style="text-align: left">$gene.transcripts[0]</td>
-          <td style="text-align: left">&ldquo;ENST00000471181.7&rdquo;</td>
-      </tr>
-  </tbody>
+<thead>
+<tr>
+<th style="text-align:left">jsonpath</th>
+<th style="text-align:left">result</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td style="text-align:left">_gid</td>
+<td style="text-align:left">&ldquo;NM_007294.3:c.4963_4981delTGGCCTGACCCCAGAAG&rdquo;</td>
+</tr>
+<tr>
+<td style="text-align:left">_label</td>
+<td style="text-align:left">&ldquo;variant&rdquo;</td>
+</tr>
+<tr>
+<td style="text-align:left">_data.type</td>
+<td style="text-align:left">&ldquo;deletion&rdquo;</td>
+</tr>
+<tr>
+<td style="text-align:left">type</td>
+<td style="text-align:left">&ldquo;deletion&rdquo;</td>
+</tr>
+<tr>
+<td style="text-align:left">publications[0].pmid</td>
+<td style="text-align:left">29480828</td>
+</tr>
+<tr>
+<td style="text-align:left">publications[:].pmid</td>
+<td style="text-align:left">[29480828, 23666017]</td>
+</tr>
+<tr>
+<td style="text-align:left">publications.pmid</td>
+<td style="text-align:left">[29480828, 23666017]</td>
+</tr>
+<tr>
+<td style="text-align:left">$gene.symbol.hugo</td>
+<td style="text-align:left">&ldquo;BRCA1&rdquo;</td>
+</tr>
+<tr>
+<td style="text-align:left">$gene.transcripts[0]</td>
+<td style="text-align:left">&ldquo;ENST00000471181.7&rdquo;</td>
+</tr>
+</tbody>
 </table>
 <h2 id="usage-example">Usage Example:</h2>
 <pre tabindex="0"><code>O.query().V([&#34;ENSG00000012048&#34;]).as_(&#34;gene&#34;).out(&#34;variant&#34;).render({&#34;variant_id&#34;: &#34;_gid&#34;, &#34;variant_type&#34;: &#34;type&#34;, &#34;gene_id&#34;: &#34;$gene._gid&#34;})